Syrian government sources said that the attacks came from the Mediterranean Sea, where both the USA and Russian Federation have built up naval forces in recent weeks amid rising tensions in Syria.
A Russian military plane vanished over Syria's Mediterranean Sea coast, authorities said Tuesday.
Russsia's Defence Ministry said the aircraft was returning to the Russian-run Hmeymim airbase in Latakia province when it disappeared from radar screens at about 11:00pm Moscow time.
"At the same time Russian air control radar systems detected rocket launches from the French frigate Auvergne which was located in that region".
The fate of the military personnel is unknown, the ministry said in a statement which was carried by Russian news agencies. In addition, Russia's Tartus naval facility is based in the Latakia governorate, as well as its Khmeimim air base. SANA reported the missiles targeting Latakia came "from the sea", citing military sources.
The Israelis had fired multiple missiles against targets in the coastal area of Latakia where Russian has based much of its military presence, including aircraft.
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An unnamed U.S. source has a different theory on the attack, telling CNN that the Russian plane was "inadvertently shot down" by Syrian government anti-aircraft artillery trying to stop the barrage of Israeli missiles.
Russian sources attributed the attacks to four F-16 fighter jets that had apparently flown over Lebanon and the Mediterranean to attack the port city.
The Syrian Observatory for Human Rights said Monday that some 140 Iranians and their allies have been killed in suspected Israeli air strikes over the last five months. The war monitoring group said it was not clear if the depot was for Iranian or Syrian forces.
Earlier in the day, Israel released satellite images of Assad's palace, Damascus International Airport and other strategic sites in Syria in what appeared to be a less than oblique threat to the Syrian ruler.
Hotlines are in place for those countries to share operational information on their deployments, but diplomats and military planners say there is still a high risk of one state inadvertently striking another country's forces. In a statement, the French military has "denied any involvement in the attack".
A spokesman for the Pentagon told CNN that the missiles were not fired by the USA military but would not speak as to who was behind the strikes.